Identifying and characterizing lung progenitor cells and their signaling niches is crucial for understanding how a healthy lung is built and maintained, how alteration of development and maintenance pathways cause or contribute to lung disease, and how disease can be prevented and damaged lung tissue restored or replaced. Identifying and characterizing lung progenitor cells and their niches has been hampered by the complex three-dimensional structure of the lung and the lack of tools to mark, follow the fate, and manipulate gene expression in individual lung cells in vivo. Here we propose to develop such tools, by adapting for use in mouse lung the systematic genetic approaches and single cell resolution genetic tools (clonal analysis) that have been used over the past decade to elucidate progenitor and stem cells and their signaling niches in the model organism Drosophila. To facilitate this, we will develop a new microscopy procedure (multidimensional microscopic molecular profiling) that allows the levels of dozens of molecular markers to be quantified at subcellular resolution on a single tissue section, the equivalent of multi-dimensional FACS analysis for intact tissues. We combine these in vivo approaches with a high throughput in vitro approach that takes advantage of recent advances in genomics and microfluidics to characterize individual lung progenitor cells and their developmental responses to the signals identified in the in vivo experiments. This combined approach is general and applicable to progenitor cells throughout the lung and other mouse tissues, although we focus on the poorly characterized progenitor cells in lung mesenchyme.